ProteinSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_PROTEIN_PROTEINSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_PROTEIN_PROTEINSUBSTITUTIONMODEL_H
 
 
#include "../AbstractSubstitutionModel.h"
#include "../SubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
 
namespace bpp
{
class ProteinSubstitutionModelInterface :
  public virtual SubstitutionModelInterface
{
public:
  virtual ~ProteinSubstitutionModelInterface() {}
 
  virtual ProteinSubstitutionModelInterface* clone() const override = 0;
 
  virtual std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const = 0;
};
 
 
class ProteinReversibleSubstitutionModelInterface :
  public virtual ProteinSubstitutionModelInterface,
  public virtual ReversibleSubstitutionModelInterface
{
public:
  virtual ~ProteinReversibleSubstitutionModelInterface() {}
 
  ProteinReversibleSubstitutionModelInterface* clone() const override = 0;
};
 
 
class AbstractProteinSubstitutionModel :
  public AbstractSubstitutionModel,
  public virtual ProteinSubstitutionModelInterface
{
public:
  AbstractProteinSubstitutionModel(
      std::shared_ptr<const ProteicAlphabet> alpha,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix) :
    AbstractSubstitutionModel(alpha, stateMap, prefix) {}
 
  virtual ~AbstractProteinSubstitutionModel() {}
 
  AbstractProteinSubstitutionModel* clone() const override = 0;
 
public:
  std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const ProteicAlphabet>(alphabet_);
  }
};
 
class AbstractReversibleProteinSubstitutionModel :
  public AbstractReversibleSubstitutionModel,
  public virtual ProteinReversibleSubstitutionModelInterface
{
public:
  AbstractReversibleProteinSubstitutionModel(
      std::shared_ptr<const ProteicAlphabet> alpha,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix) :
    AbstractReversibleSubstitutionModel(alpha, stateMap, prefix) {}
 
  virtual ~AbstractReversibleProteinSubstitutionModel() {}
 
  AbstractReversibleProteinSubstitutionModel* clone() const override = 0;
 
public:
  std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const ProteicAlphabet>(alphabet_);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_PROTEIN_PROTEINSUBSTITUTIONMODEL_H